Starting phenix.real_space_refine
on Sat Aug 23 02:06:35 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sg1_40450/08_2025/8sg1_40450.map"
  }
  resolution = 2.94
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    5669      2.51       5
     N    1490      2.21       5
     O    1621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8846
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "R"
      Number of atoms: 2172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 279, 2172
          Classifications: {'peptide': 279}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 10, 'TRANS': 268}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "A"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1750
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 77
          Classifications: {'peptide': 9}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 7}
    Chain: "E"
      Number of atoms: 1781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1781
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 64
          Unusual residues: {'CLR': 1, 'PLM': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.88, per 1000 atoms: 0.21
  Number of scatterers: 8846
  At special positions: 0
  Unit cell: (94.976, 119.568, 125.504, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1621      8.00
     N    1490      7.00
     C    5669      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 112 " - pdb=" SG  CYS R 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 160 " - pdb=" SG  CYS E 230 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Conformation dependent library (CDL) restraints added in 347.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 13 sheets defined
      36.2% alpha, 22.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'R' and resid 36 through 65
      removed outlier: 3.929A  pdb=" N   ILE R  41 " --> pdb=" O   ARG R  37 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   PHE R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 73 through 92
      removed outlier: 3.830A  pdb=" N   TRP R  77 " --> pdb=" O   VAL R  73 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE R  88 " --> pdb=" O   ALA R  84 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 92 through 101
    Processing helix  chain 'R' and resid 108 through 112
    Processing helix  chain 'R' and resid 114 through 126
    Processing helix  chain 'R' and resid 127 through 143
      removed outlier: 3.802A  pdb=" N   SER R 134 " --> pdb=" O   LEU R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 143 through 150
      removed outlier: 3.641A  pdb=" N   ASN R 149 " --> pdb=" O   VAL R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 172
      removed outlier: 3.648A  pdb=" N   ALA R 156 " --> pdb=" O   SER R 152 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 172 through 177
      removed outlier: 3.921A  pdb=" N   VAL R 176 " --> pdb=" O   SER R 172 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 214 through 251
      removed outlier: 5.043A  pdb=" N   VAL R 231 " --> pdb=" O   CYS R 227 " (cutoff:3.500A)
      Proline residue:  R 232  - end of helix
    Processing helix  chain 'R' and resid 256 through 283
      removed outlier: 3.617A  pdb=" N   ILE R 267 " --> pdb=" O   VAL R 263 " (cutoff:3.500A)
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 284 through 286
      No H-bonds generated for 'chain 'R' and resid 284 through 286'
    Processing helix  chain 'R' and resid 291 through 307
      removed outlier: 3.758A  pdb=" N   LEU R 296 " --> pdb=" O   SER R 292 " (cutoff:3.500A)
      Proline residue:  R 299  - end of helix
      removed outlier: 3.889A  pdb=" N   ALA R 307 " --> pdb=" O   ALA R 303 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 307 through 312
      removed outlier: 3.692A  pdb=" N   MET R 311 " --> pdb=" O   ALA R 307 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ASN R 312 " --> pdb=" O   ASN R 308 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 307 through 312'
    Processing helix  chain 'R' and resid 312 through 317
      removed outlier: 3.522A  pdb=" N   VAL R 317 " --> pdb=" O   PRO R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 320 through 327
      removed outlier: 4.031A  pdb=" N   PHE R 326 " --> pdb=" O   ASP R 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 8 through 25
      removed outlier: 3.566A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'G' and resid 10 through 21
      removed outlier: 4.235A  pdb=" N   MET G  21 " --> pdb=" O   GLN G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'A' and resid 6 through 30
      removed outlier: 3.853A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A  13 " --> pdb=" O   ASP A   9 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU A  28 " --> pdb=" O   ARG A  24 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A  30 " --> pdb=" O   ASP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.197A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.689A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 352
      removed outlier: 3.576A  pdb=" N   GLY A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 221 through 225
      removed outlier: 4.121A  pdb=" N   VAL E 225 " --> pdb=" O   ALA E 222 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 178 through 183
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.403A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.678A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.067A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.910A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.353A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.645A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.611A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.580A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.637A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.286A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.765A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.086A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60
      removed outlier: 5.419A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 141 through 142
      removed outlier: 3.714A  pdb=" N   VAL E 156 " --> pdb=" O   ILE E 217 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 195 through 196
      removed outlier: 6.674A  pdb=" N   TRP E 177 " --> pdb=" O   LEU E 189 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLY E 226 " --> pdb=" O   LEU E 246 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1143 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.31: 1412
        1.31 -     1.44: 2497
        1.44 -     1.56: 5028
        1.56 -     1.69: 2
        1.69 -     1.81: 95
  Bond restraints: 9034
  Sorted by residual:
  bond pdb=" C   CYS R 272 "
       pdb=" O   CYS R 272 "
    ideal  model  delta    sigma   weight residual
    1.236  1.325 -0.089 1.15e-02 7.56e+03 5.93e+01
  bond pdb=" C   THR R 268 "
       pdb=" O   THR R 268 "
    ideal  model  delta    sigma   weight residual
    1.236  1.304 -0.068 1.15e-02 7.56e+03 3.45e+01
  bond pdb=" C   TRP R 273 "
       pdb=" O   TRP R 273 "
    ideal  model  delta    sigma   weight residual
    1.237  1.189  0.047 1.19e-02 7.06e+03 1.58e+01
  bond pdb=" C   PHE R 270 "
       pdb=" O   PHE R 270 "
    ideal  model  delta    sigma   weight residual
    1.236  1.191  0.045 1.16e-02 7.43e+03 1.47e+01
  bond pdb=" C   ILE R 266 "
       pdb=" O   ILE R 266 "
    ideal  model  delta    sigma   weight residual
    1.237  1.277 -0.041 1.12e-02 7.97e+03 1.33e+01
  ... (remaining 9029 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.97: 12136
        3.97 -     7.94: 85
        7.94 -    11.91: 9
       11.91 -    15.88: 0
       15.88 -    19.85: 1
  Bond angle restraints: 12231
  Sorted by residual:
  angle pdb=" CA  PRO R 275 "
        pdb=" N   PRO R 275 "
        pdb=" CD  PRO R 275 "
      ideal   model   delta    sigma   weight residual
     112.00   92.15   19.85 1.40e+00 5.10e-01 2.01e+02
  angle pdb=" N   MET R 111 "
        pdb=" CA  MET R 111 "
        pdb=" C   MET R 111 "
      ideal   model   delta    sigma   weight residual
     112.88  103.50    9.38 1.29e+00 6.01e-01 5.29e+01
  angle pdb=" N   VAL R  73 "
        pdb=" CA  VAL R  73 "
        pdb=" C   VAL R  73 "
      ideal   model   delta    sigma   weight residual
     113.42  105.36    8.06 1.17e+00 7.31e-01 4.75e+01
  angle pdb=" N   CYS R 112 "
        pdb=" CA  CYS R 112 "
        pdb=" C   CYS R 112 "
      ideal   model   delta    sigma   weight residual
     114.56  106.02    8.54 1.27e+00 6.20e-01 4.52e+01
  angle pdb=" CA  TYR E 236 "
        pdb=" CB  TYR E 236 "
        pdb=" CG  TYR E 236 "
      ideal   model   delta    sigma   weight residual
     113.90  103.37   10.53 1.80e+00 3.09e-01 3.42e+01
  ... (remaining 12226 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 4877
       17.47 -    34.94: 408
       34.94 -    52.41: 91
       52.41 -    69.88: 14
       69.88 -    87.34: 7
  Dihedral angle restraints: 5397
    sinusoidal: 2131
      harmonic: 3266
  Sorted by residual:
  dihedral pdb=" C   TYR E 236 "
           pdb=" N   TYR E 236 "
           pdb=" CA  TYR E 236 "
           pdb=" CB  TYR E 236 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -145.35   22.75     0      2.50e+00 1.60e-01 8.28e+01
  dihedral pdb=" N   TYR E 236 "
           pdb=" C   TYR E 236 "
           pdb=" CA  TYR E 236 "
           pdb=" CB  TYR E 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  144.39  -21.59     0      2.50e+00 1.60e-01 7.46e+01
  dihedral pdb=" CB  CYS E 160 "
           pdb=" SG  CYS E 160 "
           pdb=" SG  CYS E 230 "
           pdb=" CB  CYS E 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.69  -45.69     1      1.00e+01 1.00e-02 2.89e+01
  ... (remaining 5394 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.184: 1375
       0.184 -    0.368: 19
       0.368 -    0.552: 0
       0.552 -    0.737: 0
       0.737 -    0.921: 1
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CA  TYR E 236 "
            pdb=" N   TYR E 236 "
            pdb=" C   TYR E 236 "
            pdb=" CB  TYR E 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.59    0.92 2.00e-01 2.50e+01 2.12e+01
  chirality pdb=" CA  MET R 101 "
            pdb=" N   MET R 101 "
            pdb=" C   MET R 101 "
            pdb=" CB  MET R 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.92e+00
  chirality pdb=" CA  MET R 111 "
            pdb=" N   MET R 111 "
            pdb=" C   MET R 111 "
            pdb=" CB  MET R 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.33 2.00e-01 2.50e+01 2.80e+00
  ... (remaining 1392 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS R 274 "   -0.127 5.00e-02 4.00e+02   1.73e-01 4.78e+01
        pdb=" N   PRO R 275 "    0.298 5.00e-02 4.00e+02
        pdb=" CA  PRO R 275 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO R 275 "   -0.093 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 271 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.82e+01
        pdb=" C   LEU R 271 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   LEU R 271 "    0.027 2.00e-02 2.50e+03
        pdb=" N   CYS R 272 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 275 "    0.021 2.00e-02 2.50e+03   4.21e-02 1.78e+01
        pdb=" C   PRO R 275 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   PRO R 275 "    0.027 2.00e-02 2.50e+03
        pdb=" N   TYR R 276 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1528
        2.77 -     3.30: 7933
        3.30 -     3.83: 14018
        3.83 -     4.37: 17055
        4.37 -     4.90: 30530
  Nonbonded interactions: 71064
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP G  48 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER B  74 "
            pdb=" OD1 ASP B  76 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR E 176 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OG1 THR E 151 "
            pdb=" OE1 GLU E 154 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   THR E 145 "
            pdb=" OG1 THR E 244 "
     model   vdw
     2.265 3.040
  ... (remaining 71059 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.070
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.490
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.089   9037  Z= 0.377
  Angle     :  0.890  19.854  12237  Z= 0.605
  Chirality :  0.063   0.921   1395
  Planarity :  0.007   0.173   1532
  Dihedral  : 13.730  87.345   3276
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 17.49 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.25), residues: 1105
  helix:  0.90 (0.30), residues: 351
  sheet:  0.41 (0.31), residues: 281
  loop : -0.79 (0.27), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 314 
 TYR   0.061   0.002   TYR E 236 
 PHE   0.029   0.001   PHE L 154 
 TRP   0.041   0.002   TRP R 273 
 HIS   0.013   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00534 ( 9034)
  covalent geometry    : angle       0.88963 (12231)
  SS BOND              : bond        0.00273 (    3)
  SS BOND              : angle       0.59027 (    6)
  hydrogen bonds       : bond        0.19293 (  401)
  hydrogen bonds       : angle       6.68231 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  275 PRO cc_start: 0.6854 (OUTLIER) cc_final: 0.6601 (Cg_exo)
REVERT: B  197 ARG cc_start: 0.7576 (mmt90) cc_final: 0.7074 (mpt180)
REVERT: E  235 GLU cc_start: 0.7585 (mt-10) cc_final: 0.6745 (mm-30)
  outliers start: 17
  outliers final: 15
  residues processed: 128
  average time/residue: 0.5538
  time to fit residues: 75.9389
Evaluate side-chains
  121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  275 PRO
Chi-restraints excluded: chain B residue   36 ASN
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  163 SER
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  194 SER
Chi-restraints excluded: chain E residue  198 SER
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  227 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0010
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0980
   chunk 100 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   overall best weight:    0.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  58 ASN
R  74 ASN
R 150 HIS
B 175 GLN
B 266 HIS
B 340 ASN
G  59 ASN
A 331 ASN
** E 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.157019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.109733 restraints weight = 10495.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 2.35
r_work: 0.3103 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9037  Z= 0.109
  Angle     :  0.534   7.182  12237  Z= 0.282
  Chirality :  0.042   0.208   1395
  Planarity :  0.004   0.052   1532
  Dihedral  :  5.913  59.104   1324
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.07 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.25), residues: 1105
  helix:  1.51 (0.29), residues: 362
  sheet:  0.50 (0.30), residues: 282
  loop : -0.76 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 214 
 TYR   0.018   0.001   TYR E 236 
 PHE   0.018   0.001   PHE R 259 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9034)
  covalent geometry    : angle       0.53375 (12231)
  SS BOND              : bond        0.00372 (    3)
  SS BOND              : angle       0.51155 (    6)
  hydrogen bonds       : bond        0.04425 (  401)
  hydrogen bonds       : angle       4.63208 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  215 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7605 (mm-30)
REVERT: B  219 ARG cc_start: 0.7321 (ttm-80) cc_final: 0.7044 (mtt-85)
REVERT: E  173 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7605 (t)
REVERT: E  235 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6938 (mm-30)
REVERT: E  236 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5354 (t80)
  outliers start: 19
  outliers final: 6
  residues processed: 115
  average time/residue: 0.5798
  time to fit residues: 71.3828
Evaluate side-chains
  100 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  236 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 92 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 107 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 175 GLN
E  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.151552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.107054 restraints weight = 10556.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.41
r_work: 0.2988 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9037  Z= 0.190
  Angle     :  0.596   7.525  12237  Z= 0.312
  Chirality :  0.045   0.272   1395
  Planarity :  0.004   0.054   1532
  Dihedral  :  5.868  55.072   1308
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 17.28 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.25), residues: 1105
  helix:  1.69 (0.29), residues: 362
  sheet:  0.35 (0.30), residues: 283
  loop : -0.80 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.028   0.002   TYR E 236 
 PHE   0.023   0.002   PHE R 169 
 TRP   0.016   0.002   TRP E  47 
 HIS   0.005   0.001   HIS E 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 9034)
  covalent geometry    : angle       0.59563 (12231)
  SS BOND              : bond        0.00447 (    3)
  SS BOND              : angle       0.51510 (    6)
  hydrogen bonds       : bond        0.04848 (  401)
  hydrogen bonds       : angle       4.53909 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: R  271 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.7006 (mp)
REVERT: B  214 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7380 (mtm180)
REVERT: B  215 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: B  219 ARG cc_start: 0.7439 (ttm-80) cc_final: 0.7086 (mtt-85)
REVERT: G   28 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7008 (pp)
REVERT: A   53 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6495 (mtp)
REVERT: E  203 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6941 (mtp180)
REVERT: E  235 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7133 (mm-30)
REVERT: E  246 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6899 (mp)
  outliers start: 32
  outliers final: 13
  residues processed: 127
  average time/residue: 0.5324
  time to fit residues: 72.2001
Evaluate side-chains
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain G residue   42 GLU
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  246 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0970
   chunk 84 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.7378

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R  58 ASN
R 250 ASN
B  35 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.155487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.108159 restraints weight = 10512.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 2.38
r_work: 0.3074 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2937 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9037  Z= 0.103
  Angle     :  0.500   7.660  12237  Z= 0.261
  Chirality :  0.041   0.190   1395
  Planarity :  0.004   0.050   1532
  Dihedral  :  5.500  54.238   1308
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 17.28 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.25), residues: 1105
  helix:  1.80 (0.29), residues: 368
  sheet:  0.48 (0.30), residues: 283
  loop : -0.86 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.015   0.001   TYR E 191 
 PHE   0.013   0.001   PHE E  68 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 9034)
  covalent geometry    : angle       0.50008 (12231)
  SS BOND              : bond        0.00337 (    3)
  SS BOND              : angle       0.41078 (    6)
  hydrogen bonds       : bond        0.03654 (  401)
  hydrogen bonds       : angle       4.24709 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: R   58 ASN cc_start: 0.5948 (m-40) cc_final: 0.5624 (m-40)
REVERT: R  271 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6972 (mp)
REVERT: B  214 ARG cc_start: 0.7902 (mtt-85) cc_final: 0.7383 (mtm180)
REVERT: B  215 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: B  219 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.7077 (mtt-85)
REVERT: G   28 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.7019 (pp)
REVERT: A   53 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6406 (mtp)
REVERT: E  203 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6971 (mtp180)
REVERT: E  235 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7057 (mm-30)
REVERT: E  236 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.5434 (m-80)
  outliers start: 29
  outliers final: 8
  residues processed: 127
  average time/residue: 0.5726
  time to fit residues: 77.6894
Evaluate side-chains
  114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  236 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 78 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 102 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.154896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.107314 restraints weight = 10521.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 2.37
r_work: 0.3056 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9037  Z= 0.109
  Angle     :  0.512   7.607  12237  Z= 0.264
  Chirality :  0.042   0.190   1395
  Planarity :  0.004   0.050   1532
  Dihedral  :  5.441  55.544   1308
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.01 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1105
  helix:  1.86 (0.29), residues: 368
  sheet:  0.52 (0.30), residues: 281
  loop : -0.82 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.016   0.001   TYR E 236 
 PHE   0.026   0.001   PHE R 169 
 TRP   0.012   0.001   TRP R  77 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 9034)
  covalent geometry    : angle       0.51220 (12231)
  SS BOND              : bond        0.00319 (    3)
  SS BOND              : angle       0.47053 (    6)
  hydrogen bonds       : bond        0.03707 (  401)
  hydrogen bonds       : angle       4.16446 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 106
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
REVERT: R   58 ASN cc_start: 0.5996 (m-40) cc_final: 0.5670 (m-40)
REVERT: R  271 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.7029 (mp)
REVERT: B  214 ARG cc_start: 0.7979 (mtt-85) cc_final: 0.7444 (mtm180)
REVERT: B  215 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7659 (mm-30)
REVERT: B  219 ARG cc_start: 0.7372 (ttm-80) cc_final: 0.7085 (mtt-85)
REVERT: G   28 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7020 (pp)
REVERT: E   62 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7245 (p0)
REVERT: E  203 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.7026 (mtp180)
REVERT: E  235 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7063 (mm-30)
  outliers start: 30
  outliers final: 13
  residues processed: 128
  average time/residue: 0.5668
  time to fit residues: 77.7269
Evaluate side-chains
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  271 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  232 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0970
   chunk 36 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   chunk 86 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.7578

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.107914 restraints weight = 10498.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 2.36
r_work: 0.3070 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9037  Z= 0.103
  Angle     :  0.514   9.666  12237  Z= 0.263
  Chirality :  0.042   0.182   1395
  Planarity :  0.004   0.049   1532
  Dihedral  :  5.385  58.259   1308
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.22 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.25), residues: 1105
  helix:  1.88 (0.29), residues: 368
  sheet:  0.56 (0.30), residues: 281
  loop : -0.79 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.016   0.001   TYR E 236 
 PHE   0.029   0.001   PHE R 169 
 TRP   0.012   0.001   TRP R  77 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9034)
  covalent geometry    : angle       0.51448 (12231)
  SS BOND              : bond        0.00283 (    3)
  SS BOND              : angle       0.53509 (    6)
  hydrogen bonds       : bond        0.03573 (  401)
  hydrogen bonds       : angle       4.09781 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
REVERT: R   58 ASN cc_start: 0.5836 (m-40) cc_final: 0.5557 (m-40)
REVERT: B  214 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7356 (mtm180)
REVERT: B  215 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7709 (mm-30)
REVERT: B  219 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.7102 (mtt-85)
REVERT: G   28 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.7066 (pp)
REVERT: A   53 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7117 (mmm)
REVERT: E   62 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7262 (p0)
REVERT: E  203 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7050 (mtp180)
REVERT: E  235 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7084 (mm-30)
  outliers start: 32
  outliers final: 18
  residues processed: 130
  average time/residue: 0.5370
  time to fit residues: 74.7368
Evaluate side-chains
  123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  232 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:   30.0000
   chunk 60 optimal weight:    5.9990
   chunk 103 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 94 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B  88 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.150284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.103110 restraints weight = 10633.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.34
r_work: 0.2994 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9037  Z= 0.208
  Angle     :  0.613  10.071  12237  Z= 0.316
  Chirality :  0.046   0.241   1395
  Planarity :  0.004   0.056   1532
  Dihedral  :  5.793  58.076   1307
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.53 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.25), residues: 1105
  helix:  1.79 (0.28), residues: 368
  sheet:  0.37 (0.29), residues: 282
  loop : -0.88 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 314 
 TYR   0.029   0.002   TYR E 236 
 PHE   0.017   0.002   PHE E  68 
 TRP   0.015   0.002   TRP E  47 
 HIS   0.008   0.001   HIS E 233 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 9034)
  covalent geometry    : angle       0.61300 (12231)
  SS BOND              : bond        0.00467 (    3)
  SS BOND              : angle       0.64964 (    6)
  hydrogen bonds       : bond        0.04711 (  401)
  hydrogen bonds       : angle       4.31621 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: B  214 ARG cc_start: 0.7968 (mtt-85) cc_final: 0.7438 (mtm180)
REVERT: B  215 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7714 (mm-30)
REVERT: G   28 ILE cc_start: 0.7225 (OUTLIER) cc_final: 0.6987 (pp)
REVERT: A   53 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7142 (mmm)
REVERT: E   62 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7276 (p0)
REVERT: E  203 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7113 (mtp180)
REVERT: E  216 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7532 (p)
REVERT: E  232 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8648 (tm-30)
REVERT: E  235 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7448 (mt-10)
  outliers start: 32
  outliers final: 17
  residues processed: 127
  average time/residue: 0.6117
  time to fit residues: 82.7652
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  112 CYS
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  216 THR
Chi-restraints excluded: chain E residue  232 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 56 optimal weight:    5.9990
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0070
   chunk 64 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.7602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.153960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.106695 restraints weight = 10505.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 2.36
r_work: 0.3035 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   9037  Z= 0.106
  Angle     :  0.530  12.277  12237  Z= 0.270
  Chirality :  0.042   0.204   1395
  Planarity :  0.004   0.052   1532
  Dihedral  :  5.471  59.066   1307
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.27 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1105
  helix:  1.89 (0.29), residues: 368
  sheet:  0.42 (0.30), residues: 282
  loop : -0.83 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 314 
 TYR   0.016   0.001   TYR E 236 
 PHE   0.028   0.001   PHE R 169 
 TRP   0.014   0.001   TRP R  77 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9034)
  covalent geometry    : angle       0.52973 (12231)
  SS BOND              : bond        0.00309 (    3)
  SS BOND              : angle       0.45551 (    6)
  hydrogen bonds       : bond        0.03749 (  401)
  hydrogen bonds       : angle       4.16136 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 0.370 
Fit side-chains
REVERT: R   58 ASN cc_start: 0.5860 (m-40) cc_final: 0.5523 (m-40)
REVERT: B  214 ARG cc_start: 0.7956 (mtt-85) cc_final: 0.7371 (mmm-85)
REVERT: B  215 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7640 (mm-30)
REVERT: B  217 MET cc_start: 0.8390 (pmt) cc_final: 0.7747 (ppp)
REVERT: G   28 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.7015 (pp)
REVERT: A   53 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7060 (mmm)
REVERT: E   62 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7203 (p0)
REVERT: E  203 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7237 (mtp180)
REVERT: E  235 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7029 (mm-30)
  outliers start: 27
  outliers final: 15
  residues processed: 126
  average time/residue: 0.5739
  time to fit residues: 77.3581
Evaluate side-chains
  123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  123 MET
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  203 ARG
Chi-restraints excluded: chain E residue  205 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 27 optimal weight:    9.9990
   chunk 100 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   chunk 81 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.154676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.107955 restraints weight = 10545.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 2.33
r_work: 0.3046 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9037  Z= 0.111
  Angle     :  0.530  13.307  12237  Z= 0.269
  Chirality :  0.042   0.181   1395
  Planarity :  0.004   0.053   1532
  Dihedral  :  5.235  58.964   1306
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 20.10 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.25), residues: 1105
  helix:  1.94 (0.29), residues: 366
  sheet:  0.53 (0.30), residues: 280
  loop : -0.81 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 314 
 TYR   0.016   0.001   TYR E 236 
 PHE   0.033   0.001   PHE R 169 
 TRP   0.013   0.001   TRP R  77 
 HIS   0.003   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9034)
  covalent geometry    : angle       0.53017 (12231)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.63939 (    6)
  hydrogen bonds       : bond        0.03670 (  401)
  hydrogen bonds       : angle       4.09841 ( 1143)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.364 
Fit side-chains
REVERT: R   58 ASN cc_start: 0.5848 (m-40) cc_final: 0.5551 (m-40)
REVERT: B  214 ARG cc_start: 0.7921 (mtt-85) cc_final: 0.7270 (mmm-85)
REVERT: B  215 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7655 (mm-30)
REVERT: B  217 MET cc_start: 0.8321 (pmt) cc_final: 0.7879 (pmm)
REVERT: G   28 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.7001 (pp)
REVERT: A   53 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6906 (mmm)
REVERT: E   62 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7281 (p0)
REVERT: E   89 GLU cc_start: 0.7797 (pt0) cc_final: 0.7166 (pp20)
REVERT: E  235 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6944 (mm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 124
  average time/residue: 0.5760
  time to fit residues: 76.3267
Evaluate side-chains
  121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  205 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 13 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B  35 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.151352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.104075 restraints weight = 10552.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.34
r_work: 0.3019 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9037  Z= 0.171
  Angle     :  0.591  14.294  12237  Z= 0.301
  Chirality :  0.044   0.231   1395
  Planarity :  0.004   0.054   1532
  Dihedral  :  5.553  58.995   1306
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.31 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1105
  helix:  1.91 (0.29), residues: 360
  sheet:  0.43 (0.30), residues: 281
  loop : -0.80 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 314 
 TYR   0.023   0.002   TYR E 236 
 PHE   0.014   0.002   PHE R 190 
 TRP   0.013   0.002   TRP E  47 
 HIS   0.005   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9034)
  covalent geometry    : angle       0.59100 (12231)
  SS BOND              : bond        0.00410 (    3)
  SS BOND              : angle       0.59291 (    6)
  hydrogen bonds       : bond        0.04368 (  401)
  hydrogen bonds       : angle       4.24851 ( 1143)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2210 Ramachandran restraints generated.
    1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.301 
Fit side-chains
REVERT: B  214 ARG cc_start: 0.7894 (mtt-85) cc_final: 0.7367 (mmm-85)
REVERT: B  215 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7692 (mm-30)
REVERT: B  217 MET cc_start: 0.8283 (pmt) cc_final: 0.7845 (pmm)
REVERT: G   28 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6983 (pp)
REVERT: A   53 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6962 (mmm)
REVERT: E   62 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7186 (p0)
REVERT: E  235 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7307 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 123
  average time/residue: 0.5958
  time to fit residues: 78.3561
Evaluate side-chains
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  263 VAL
Chi-restraints excluded: chain R residue  282 LEU
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain G residue   28 ILE
Chi-restraints excluded: chain A residue   53 MET
Chi-restraints excluded: chain A residue  332 VAL
Chi-restraints excluded: chain E residue   45 LEU
Chi-restraints excluded: chain E residue   62 ASP
Chi-restraints excluded: chain E residue   64 VAL
Chi-restraints excluded: chain E residue  140 VAL
Chi-restraints excluded: chain E residue  156 VAL
Chi-restraints excluded: chain E residue  173 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  232 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 87 optimal weight:    0.0060
   chunk 54 optimal weight:    0.8980
   chunk 12 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   overall best weight:    1.3800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
R 250 ASN
B 175 GLN
A 304 GLN
E  82 GLN
E 232 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.152115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.104910 restraints weight = 10436.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.33
r_work: 0.3034 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9037  Z= 0.139
  Angle     :  0.561  12.966  12237  Z= 0.286
  Chirality :  0.043   0.214   1395
  Planarity :  0.004   0.053   1532
  Dihedral  :  5.478  58.730   1306
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.73 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1105
  helix:  1.92 (0.29), residues: 361
  sheet:  0.46 (0.30), residues: 281
  loop : -0.77 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 314 
 TYR   0.022   0.001   TYR E 236 
 PHE   0.028   0.001   PHE R 169 
 TRP   0.013   0.001   TRP R  77 
 HIS   0.004   0.001   HIS E  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9034)
  covalent geometry    : angle       0.56146 (12231)
  SS BOND              : bond        0.00358 (    3)
  SS BOND              : angle       0.61918 (    6)
  hydrogen bonds       : bond        0.04098 (  401)
  hydrogen bonds       : angle       4.20004 ( 1143)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3508.49 seconds
wall clock time: 60 minutes 41.41 seconds (3641.41 seconds total)